Additive profiles. The profile functions in MUSCLE require amino acid frequencies for each column. Here we show the alignment of two profiles X and Y, giving a new profile Z. Note that the count nZi for amino acid i in a given column of Z is the sum of the counts in the child profiles, i.e. nZi = nXi + nYi. In terms of frequencies, this becomes f Zi = NXf Xi /NZ + NYf Yi/NZ, where NX, NY, NZ are the number of sequences in X, Y and Z respectively. Therefore, given a suitable sequence weighting scheme, it is possible to compute frequencies in Z from the frequencies in X and Y. This avoids the step of building an explicit multiple alignment for Z in order to compute frequencies, as done in CLUSTALW and MAFFT.
Edgar BMC Bioinformatics 2004 5:113 doi:10.1186/1471-2105-5-113